Chlamydia trachomatis (CT) is one of three species in the Chlamydia family of gram-negative bacteria. CT is an obligate intracellular pathogen, which can only reproduce inside its host cell. CT includes at least two biovars, trachoma and lymphogranuloma venereum (LGV). The trachoma biovar includes at least 14 serovars whose infection is primarily in epithelial cells of mucous membranes. LGV includes at least four serovars that can invade lymphatic tissue. There are an estimated 3 million CT infections annually, most of which are asymptomatic. In the United States, the national rate of CT infection in 2006 was about 348 cases per 100,000 people, which was a 5.6% increase from 2005.
Neisseria gonorrhoeae (NG) is a gram-negative oxidase-positive diplococcus bacterium. There are an estimated 700,000 NG infections annually. The NG infection rate in the United States also increased by over 5% from 2005 to 2006, to about 121 cases per 100,000 people. Symptoms of NG infection differ according to the site of infection, although a majority of infected women and a significant proportion of infected men are asymptomatic.
If left untreated, both CT and NG infections can lead to pelvic inflammatory disease and infertility in women, and urethritis in men. The Centers for Disease Control (CDC) currently recommends annual CT screening for all sexually active women under 26.
Many current CT/NG tests are complex assays requiring several different apparatuses and are therefore run in batch format. Batch format tests are not run on demand, and results are therefore typically not received for several days, during which time an infection can be spread. In addition, the leading tests detect CT genes located on a plasmid. While those sequences are present in higher copy, they are also more easily lost, as demonstrated by the emergence and rapid spread of a variant CT strain in Sweden that escaped detection because it had a plasmid deletion. See, e.g., Seth-Smith et al., BMC Genomics, 10:239 (2009). In addition, because species in the Neisseria family are closely related, some current tests have a high rate of false positives for NG.
Genomic copy number analysis usually refers to the process of analyzing data produced by assays for DNA copy number variation at specific genomic loci in a subject's sample. Such analysis helps detect copy number variation at specific loci that may cause, increase risk of, or be correlated with diseases, such as cancer. Copy number variation can be detected with various types of tests such as fluorescent in situ hybridization, comparative genomic hybridization and with high-resolution array-based tests based on array comparative genomic hybridization (aCGH) and SNP array technologies. Array-based methods have been accepted as the most efficient in terms of their resolution and high-throughput nature.